Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial

C Ludwig, L Gillet, G Rosenberger, S Amon… - Molecular systems …, 2018 - embopress.org
Many research questions in fields such as personalized medicine, drug screens or systems
biology depend on obtaining consistent and quantitatively accurate proteomics data from …

SWATH‐MS as a tool for biomarker discovery: From basic research to clinical applications

SI Anjo, C Santa, B Manadas - Proteomics, 2017 - Wiley Online Library
In the era of quantitative proteomics, where mass spectrometry plays a pivotal role, in
particular associated with the use of data‐independent acquisition, it is time to perform an …

The human plasma proteome draft of 2017: building on the human plasma PeptideAtlas from mass spectrometry and complementary assays

JM Schwenk, GS Omenn, Z Sun… - Journal of proteome …, 2017 - ACS Publications
Human blood plasma provides a highly accessible window to the proteome of any individual
in health and disease. Since its inception in 2002, the Human Proteome Organization's …

Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques

JG Meyer, B Schilling - Expert review of proteomics, 2017 - Taylor & Francis
Introduction: While selected/multiple-reaction monitoring (SRM or MRM) is considered the
gold standard for quantitative protein measurement, emerging data-independent acquisition …

Acquisition and analysis of DIA-based proteomic data: A comprehensive survey in 2023

R Lou, W Shui - Molecular & Cellular Proteomics, 2024 - ASBMB
Data-independent acquisition (DIA) mass spectrometry (MS) has emerged as a powerful
technology for high-throughput, accurate, and reproducible quantitative proteomics. This …

SWATH-MS-based proteomics: strategies and applications in plants

MX Chen, Y Zhang, AR Fernie, YG Liu, FY Zhu - Trends in Biotechnology, 2021 - cell.com
Most applied proteomic approaches require labeling steps. Recent technological advances
provide an alternative label-free proteomics approach: SWATH-MS. This powerful tool is …

Comparative analyses of data independent acquisition mass spectrometric approaches: DIA, WiSIM‐DIA, and untargeted DIA

F Koopmans, JTC Ho, AB Smit, KW Li - Proteomics, 2018 - Wiley Online Library
Data‐independent acquisition (DIA) is an emerging technology for quantitative proteomics.
Current DIA focusses on the identification and quantitation of fragment ions that are …

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS

G Rosenberger, Y Liu, HL Röst, C Ludwig, A Buil… - Nature …, 2017 - nature.com
Consistent detection and quantification of protein post-translational modifications (PTMs)
across sample cohorts is a prerequisite for functional analysis of biological processes. Data …

Data‐independent acquisition proteomics methods for analyzing post‐translational modifications

Y Yang, L Qiao - Proteomics, 2023 - Wiley Online Library
Protein post‐translational modifications (PTMs) increase the functional diversity of the
cellular proteome. Accurate and high throughput identification and quantification of protein …

Clinically relevant post-translational modification analyses—maturing workflows and bioinformatics tools

D Pascovici, JX Wu, MJ McKay, C Joseph… - International journal of …, 2018 - mdpi.com
Post-translational modifications (PTMs) can occur soon after translation or at any stage in
the lifecycle of a given protein, and they may help regulate protein folding, stability, cellular …